So far I've been running both plugins with no problems. I think W3TC only changes .htaccess when you change your settings, so you should only need to disable the "Remove write permissions" when you're changing W3TC settings.
@graphics616, I note that your errors seems to be related to W3TC installation. It's certainly the case that you need to allow W3TC to write to .htaccess during installation. I'd try disabling "Remove write permissions" in Better WP Security during the W3TC install and setup, then you should be able to re-enable that protection.
Someone else feel free to chime in if I'm mistaken.